The biggest problem with mobipocket, format-wise, is that (as far as I know) it only allows to set vertical spacing above elements, so if you want to have some space below a chapter heading, or a piece of poetry, or an indented block... you have to set the space (with "height") in the element below that (a paragraph, a div, or whatever).

I create mobipocket books with html2mobi, from very simple HTML. Basically, I use only <P>, <DIV>, <I>, <B>, <Hx>, <A>, <IMG>... (sometimes <BR>, <SUP>, <HR>... if needed), and the only properties are "align", "height" (for vertical space) and "width" (for first-line paragraph indent (and "href" for <A>, "src" for <IMG>). The pagebreaks I add them with <mbp:pagebrak/>, and the guide items are defined in the <head>. If someone is interested in seeing any of my source files, just ask by PM.

EDIT: Oh, and I encode everything in ASCII, so I write &mdash;, &eacute;, etc. (or rather let a program write them).